Elegant Solutions {ReadingNotes}

Elegant Solutions: Ten Beautiful Experiments in Chemistry by Philip Ball - ISBN 0854046747 - Royal Society of Chemistry 2005

Motivation

Generally wanting to improve the precision of each layer of my scientific model of reality (mainly going down the scale, from bioloy to chemistry to physics), having started the Key Experiments focusing on cognitive science and finally having already browse through The Self-Made Tapestry: Pattern Formation in Nature by the same author.

Pre-reading model

Draw a schema (using PmGraphViz or another solution) of the situation of the area in the studied domain before having read the book.

Reading

• Introduction
  • "The Greek word organon means an instrument or engine: Bacon's new engine [his Novum Organum] was the device that would churn out a new philosophical understanding of the world, and it is characteristic of Bacon that he should choose a metaphor from applied science to describe his project. " (p1)
  • "for Bacon, the notion of 'experiment' never lost touch with its roots in the concept of 'art'; or techne, the Greek word from which 'technology'; is derived. It was about making things; and that had, ever since ancient times, the taint of wizardry about it. " (p4)
  • "until the Renaissance, it was extremely rare that an experiment would be conducted to test an idea: it was simply a way of demonstrating that you were right. " (p5)
  • "Philosopher of science Joachim Schummer has estimated that there are more - many more - scientific papers published in chemistry than in any other scientific discipline. " (p7)
    • Research Topics in History and Philosophy of Science from Joachim Schummer webpage
  • "a 'beautiful' experiment in chemistry: the beauty need not lie in the conception or the execution, but in the product. " (p7)
  • "all of the examples [...] chosen do have some broader significance in chemistry or in science more generally. " (p9)
  • "Experiments give a concrete framework on which to hang stories about the histories of science - but sometimes those stories come to have a strong element of invention about them, which in itself says something interesting about how we understand both science and history. " (p10)

Section 1 Asking Questions of Nature

• 1 How Does Your Garden Grow?
  • "Jan Baptista van Helmont, a Flemish physician, demonstrates that everything tangible is ultimately made from water, by growing a willow tree in a pot of soil nourished by nothing but pure water." (p11)
  • "Perhaps the first thing school students of chemistry learn is that it is all about weighing things. " (p11)
  • brief description of the experiment itself page 18
  • "like Nicholas de Cusa he [Jan Baptista van Helmont] was thinking about how to exclude influences that could corrupt his results. " (p18)
  • "The experiment was beautiful because of the clarity of its concept: it was hard to see what could possibly have been overlooked, or what could have led to any error. That beauty is enhanced by the reliance on quantification, which transforms an anecdote into a scientific result. " (p19)
  • "It is hard to fault either the experimental design or the logic of the interpretation; we can't reasonably expect van Helmont to have come to any other conclusion. There is surely a humbling message in this for scientists today: if an important part of the puzzle is missing, what seems 'obvious' may in fact be fundamentally fallacious. " (p19)
• 2 An Element Compounded
  • "Cavendish's claim to the discovery that water is a compoun" (p22)
  • "The problem is that when everyone believes something, no one bothers to check it. " (p22)
  • "He understood the meaning of accuracy and precision, and realised that all experiments have a finite and unavoidable margin of error. " (p27)
  • "This is arguably Cavendish's greatest contribution to experimental science: an attention to numerical detail that keeps the experimenters' claims in proportion to what their methods justify. " (p28)
  • "Cavendish was in no hurry in any case. For him, publication was not the objective, and he seems blithely unconcerned about securing any claims to priority. He seems to have adopted the approach advocated by his colleague William Heberden, who said that the happiest writer wrote <<always with a view to publishing, though without ever doing so>>. " (p29)
  • see also H2O - The Mystery, Art, and Science of Water: The Chemistry of Water: Electrolysis by Jill Granger
  • Peter Wothers: Just Add Water, Australian National University, Australian Broadcasting Corporation, August 2009
• 3 New Light
  • "Two dissolved elements may be parted if one of them forms an insoluble compound while the other does not: the one can be precipitated and collected by filtering, while the other remains dissolved in solution. " (p44)
  • "The Curies found that in fact pitchblende seemed to contain two new 'active' elements. One of them was chemically similar to barium, precipitating when chloride was added to a solution of the mixture to produce insoluble barium chloride. The other element seemed instead to 'follow' the element bismuth. " (p44)
  • "They finally prepared a sample with 900 times more radioactivity than pitchblende, and Demarc'ay saw at last a new spectral line [using spectroscopy]. Here was their evidence. " (p45)
  • "she was even moved tentatively to suggest a virtual heresy: might radioactivity violate the first law of thermodynamics, the stipulation that energy can be neither created nor destroyed? " (p48)
  • "These [Julius Elster and Hans Geitel] were the first experiments conducted underground to exclude penetrating environmental effects, pre-empting today's searches for neutrinos and other exotic subatomic particles in deeply buried laboratories. " (p49)
  • "[Julius Elster and Hans Geitel] saw no change in the activity of their radioactive samples, which led them to believe that the energy must be emanating 'from the atom itself'. Radioactivity was, in other words, a form of atomic energy. " (p49)
  • "before long, the Curies' entire laboratory was measurably radioactive, and their notebooks are still too 'hot' for safe handling. " (p52-53)
  • on Becquerel, first mentionned page 41, see La marche des sciences on Henri Becquerel on France Culture, September 2009
• 4 Radiation Explained
  • "Ernest Rutherford satisfies his long obsession with the alpha particles emitted by radioactive materials - particles that he was the first to identify and to name - by demonstrating conclusively that they consist of the nuclei of helium atoms. " (p54)
  • "The elegance of his practical work seems to have derived from a rare conjunction of clarity of conception and pleasure in finding a way to physically realise it. " (p55)
  • "There appeared to be some kind of fertile feedback between Rutherford's hands and his mind, so that his ability to visualize and to fabricate a piece of apparatus helped the experiment to take shape in his head. " (p55-56)
  • "At heart he was a Victorian, content to build his equipment with sealing wax and string, and at the end of his career this made him seem almost a hidebound curmudgeon, deploring the commercialization of science and turning down large industrial grants in the belief that the best science was done on a shoestring. " (p56)
  • "Rutherford realised that this disappearance of 'parent elements' and the accumulation of 'daughter elements' could be used as a kind of clock to estimate the ages of minerals. " (p58)
  • "Rutherford's artificially induced splitting of the atom in 1919, to the realization that this 'nuclear fission' could be an awesome source of energy, to the bright promise of nuclear power and the grim reality of nuclear warfare. " (p66)
  • "Bohr's quantum atom, in which the circuits of the electrons around the nucleus were confined to specific, quantized orbits, led to an understanding of how the disposition of electrons in atoms gives rise to the unique chemical properties that distinguish one element from another, rationalizing the familiar twin-towered arrangement of the periodic table. " (p66)
  • What are the Radioactive Byproducts of Depleted Uranium (Uranium-238)? at Canadian Coalition for Nuclear Responsibility (CCNR)
• 5 The Elements Came in One by One
  • "The feat of conducting chemistry one atom at a time with ephemeral seaborgium stretches the techniques of chemical analysis about as far as they will go. " (p67)
  • "the story of chemistry is all about how elements behave - how they react with one another to form combinations of elements, how they may be shuffled and grouped into symphonies of atoms. " (p68)
  • "It is called the periodic table table because certain chemical properties recur periodically as one progresses through the list of increasing atomic number from 1 (hydrogen) to 92 (uranium). " (p74-75)
  • "Seaborg's intuition was borne out as the Berkeley team continued to extend the table, using each new element as the raw material for another further along the row." (p74-75)
    • could this be associated to a more fundamental phylogenic model?
  • "How on earth do you spot one atom among a billion others? [...] The most important is called ion-exchange chromatography, which involves passing a solution containing ions of the various elements through a column packed with resin-coated beads. " (p76)
  • "The best way to speed everything up is to make it automated. This approach to rapid radiochemistry began in the late 1960s, both in the American and in the Soviet laboratories. " (p81)
  • "There are four basic steps in any procedure of this sort:
    • 1. Synthesize the element by ion-beam collisions with a target.
    • 2. Transport the element, or its compounds, rapidly to the analytical chemistry apparatus.
    • 3. Isolate and purify the element as quickly as possible.
    • 4. Detect the element by monitoring its radioactive decay." (p81)
  • "This journey into the 'artificial' periodic table shows no signs of approaching an end. " (p89)
  • "In some ways this is chemistry as we have always known it: the investigation of how atoms combine. But in another sense it is something quite new, for these are atoms that nature cannot make. " (p90)
  • in the news, Superheavy Element 114 Confirmed: A Stepping Stone to the Island of Stability, Berkeley Lab News Center September 2009
• Divertissement 1 The Chemical Theatre
  • "the immediacy of a well-conceived experimental demonstration connects with our innate ability to comprehend by visual revelation: seeing is <<believing>>. " (p92)
  • "Ritual links us to the past: history gives an action a form of confirmation. The experimental scientist typically undergoes an apprenticeship that is only partly about acquiring useful skills; it is also concerned with the inheritance of a tradition. " (p99)
    • see also my Shift on Reinventing academic publishing online. Part I: Rigor, relevance and practice on how "The modern academic system has become almost a training ground for conformity."
  • Reaction of Sodium with Chlorine

Section 2 Posing New Questions

• 6 Molecules Take Shape
  • "[Louis Pasteur] studies of crystalline salts prepared from the by-products of wine-making thus lead Pasteur to a crucial insight about the threedimensional structures of carbon-based molecules. " (p101)
  • "Pasteur claimed that <<for an instant my heart stopped beating>>. But then he looked more closely and noticed that they were asymmetric in both senses: some were lefthanded, and some right-handed, in contrast to the single handedness of tartrate. And so (Pasteur said), the answer to this riddle struck him in a flash. " (p108)
  • "A molecule's <<stereochemistry>> refers to the arrangement of its atoms in three-dimensional space: molecules containing the same atoms and the same connections between them, but different three-dimensional shapes, are known as stereoisomers. " (p111)
  • "Two stereoisomers that are mirror images of one another are called enantiomers (from the Greek enantios, opposite). " (p111)
  • "the property of molecular handedness [name is] derived [...] from the Greek word for hand, kheir: this sort of asymmetry is called chirality. " (p111)
  • "if Pasteur was wrong to think that only nature can generate chiral molecules, nevertheless it remains true that she is a lot better at it than we are. " (p118)
  • Chiral Molecules from the University of Nottingham
• Divertissement 2 Myths and Romances
  • "the real question is why chemistry is so prone to these fancies - much more so, it seems, than other science. " (p119)
  • "all of scientific history is seen through the lens of the present, so that historical ideas are labelled 'good' or 'bad' depending on their congruence with contemporary scientific understanding. " (p123)
  • "this form of science history has a triumphalist agenda that asks us to marvel at how far we have progressed beyond the ignorance and murk of former times. It says 'What a piece of work is man!'" (p123)
• 7 Life and How To Make It
  • "suddenly such a feat [generating an organism spontaneously in a test tube] seemed a whole lot less impossible: it was, you might say, the 'impossible' of an exceedingly hard problem, not the 'impossible' of a transgression against nature. " (p125)
  • "Typically, however, these experiments on prebiotic mixtures remained wedded to the idea that the early atmosphere was oxidizing, and so they used ingredients such as carbon dioxide and nitrogen. " (p129)
  • "Without knowing about Oparin's ideas, Urey came to the conclusion in 1951 that the early Earth must have had a reducing atmosphere. " (p130)
  • "<<The fact that the experiment is so simple that a highschool student can almost reproduce it>>, says Miller, <<is not a negative at all. The fact that it works and is so simple is what is so great about it.>>" (p131)
  • "Not even the young, optimistic Miller could have anticipated how quickly his flasks would cook up something interesting. Overnight, the water turned red: a sure signature of complex chemicals in the broth. " (p133)
  • "In total, 10-15% of the carbon in the methane gas was converted into organic compounds within Miller's apparatus. " (p134)
  • "Since then, chemists have devised ingenious ways of making all the key building blocks of life's molecules - amino acids and nucleotides, the basic structural units of DNA and RNA - from simple precursor molecules under conditions that are more or less plausibly 'prebiotic'. " (p135)
  • "The Earth has apparently been showered with these substances [carbonaceous meteorite] since its earliest days, and some researchers believe that the principal source of life's building blocks could have been this extraterrestrial delivery, rather than formation in situ. " (p136)
  • "The discovery in the 1980s that RNA molecules can indeed act as catalysts in cells today made it seem considerably more likely that the very earliest 'proto-life' went through a stage that looked something like the RNA World. " (p137)
  • "<<It was the Miller experiment>>, say 'exobiologists' Jeffrey Bada and Antonio Lazcano, <<that almost overnight transformed the study of the origin of life into a respectable field of enquiry.>>" (p137-138)
  • see also
    • my notes on Protocells: Bridging Nonliving and Living Matter MIT Press 2008
    • The EvoGrid: The Evolution Technology Grid
    • Amino Acids Department of Biochemistry and Molecular Biophysics, University of Arizona
• 8 Not so Noble
  • "the consensus view of chemists worldwide: <<the unreactivity of the noble gas elements belongs to the surest of all experimental results>>. " (p140)
  • "Forty years later the general opinion had hardly changed, which is why it took great boldness to do what Neil Bartlett did in 1962. It was, however, a boldness born of straightforward, textbook reasoning. " (p141)
  • "The beauty of the experiment stems from that simplicity, that recognition and embracing of opportunity - that ingenuous leap into the unknown. " (p141)
  • "The reason for the inactivity of these elements fell out of the quantum-mechanical explanation for the periodic table and for chemical bonding that was developed in the 1920s. " (p141)
  • "The physicists Niels Bohr and Arnold Sommerfeld rationalized these ideas by showing that the electron-shell structure of atoms emerges directly out of quantum theory. " (p141)
  • "Roughly speaking, the electrons in an atom's outer shell get held increasingly tightly from the left to the right of a row in the periodic table, because the positive charge on the nucleus (which is what binds the electrons in the atom) increases along the row" (p143)
  • "The first ionization potential of xenon is in fact 12.13 eV. So, Bartlett figured, if PtF6 can truly ionize O₂ to make O₂⁺, it should be capable of doing the same to xenon. " (p145)

Section 3 The Art of Making Things

• 9 Nature Rebuilt
  • "As chemists began gradually to uncover the principles governing the shapes of organic molecules, organic synthesis acquired a new purpose beyond the production of useful materials. It became a way of checking that the molecular structure assigned to an organic compound was correct. " (p156)
  • "The complex frameworks of the molecules must be constructed step by step: each strut, girder and bridge of the backbone is painstakingly assembled, and the frame is adorned with its various molecular accoutrements. For the purposes of structure-checking, this stepwise procedure was the whole point. " (p156)
  • "If each step in a ten-stage synthesis is 80% efficient (which would be pretty good going in organic chemistry), then only 10% of the starting material is transformed into the final product. This wastage pushes up the cost of the process. So as organic syntheses became increasingly complex and multi-staged, chemists were ever more pressed to keep them economically viable. " (p157)
  • "Difficult organic syntheses forced chemists to devise new strategies and thereby to broaden the battery of techniques at their disposal for making other molecules. " (p160)
  • "There are often good practical reasons for devising a total synthesis of a pharmaceutical compound, even if the route is not an economically viable one. " (p160)
  • "As in all experiments, the art lies in this strategy. That is the difficult part. " (p165)
  • "vision of the art of synthesis guided Woodward to one of his most renowned manoeuvres, the so-called 'ring tactic', in which he would 'freeze' part of a molecule by making a ring, preventing it from any untoward gymnastics, only at the end to break the ring open and release it." (p165-166)
  • "Synthetic chemists who labour away making the most obscure, intricate and apparently useless molecules like to justify their efforts by claiming that they learn a lot along the way. The Woodward-Hoffmann rules show how profound such serendipitous discoveries can be. " (p171)
• 10 Platos Molecules
  • "three-dimensional molecules are truly a form of atomic architecture." (p178)
  • "arguably it was dodecahedrane that first got the ball rolling, by showing that organic chemistry is literally multi-faceted and that carbon can be sculpted and moulded in ways that would have delighted the ancient philosophers. " (p90)
• Coda Chemical Aesthetics
  • "An experiment in chemistry can be beautiful not because of conceptual elegance or demonstrative power but merely because it is lovely to watch. " (p192)
  • "what would happen if a truly artistic aesthetic were to become wedded to chemical creativity: if a plastic artist as eclectic as Picasso were to somehow acquire the skills of a Woodward. That would be something to see. " (p196)

See also

• Chemistry
  • including Chemistry#Computation previously present on this page
• Kary Mullis celebrates the experiment at TED 2002
• periodic table
  • Visual Elements an arts and science collaborative project from the RSC which explores the diversity of elements in a unique and innovative manner.
  • Animated Periodic Table
  • Timeline of Element Discovery in History of Chemistry by Anne Marie Helmenstine, About.com
  • History of the periodic table on Wikipedia
• computational quantum chemistry
  • The Molecular Modelling Toolkit (MMTK) Open Source program library for molecular simulation applications.
  • Open Babel chemical toolbox designed to speak the many languages of chemical data.
  • PyQuante open-source suite of programs for developing quantum chemistry methods.
• Chemistry at Open Yale Courses
• Chemistry: A Volatile History, BBC January 2010

Experiments Tools

• protocols
  • Protocol Online Your lab's reference book
  • myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.
  • SpringerProtocols database of reproducible laboratory protocols in the Life and Biomedical Sciences
    • with videos
  • Current Protocols The Fine Art of Experimentation
  • Nature Protocols online resource for protocols, including authoritative, peer-reviewed Nature Protocols and an interactive Protocols Network.
• deduction and induction frameworks
  • overall [{Wikipedia:Computational science]]
  • Triana Open Source Problem Solving Software
  • GridLab A Grid Application Toolkit and Testbed
    • finished project, check the resulting tools
  • Transitional Computer captures advanced domain knowledge into focused ICT service applications that run on common, nationally-scalable ICT platforms
  • Adams Robot Scientist
  • Eureqa by Cornell Computational Synthesis Laboratory
    • software tool for detecting equations and hidden mathematical relationships in your data
  • ZunZun.com Online Curve Fitting and Surface Fitting
    • curve fit and surface fit your 2D and 3D data online with a rich set of error histograms, error plots, curve plots, surface plots, contour plots, VRML, and source code.
  • Enabling Desktop Grids for e-Science (EDGeS) integrated Grid infrastructure that seamlessly integrates a variety of Desktop Grids with EGEE type of service Grids
• VLE (Virtual Environment Laboratory)
  • multimodeling, simulation platform based on the discrete event formalism DEVS (Discrete Event System Specification).

Overall remarks and questions

• the book is written in chronological order making it easier to follow thanks to a logical structure
  • every chapter seems to stress on factors affecting the scientific method
• projects of chemistry printer
  • A general system in which you input a sequence/compound structure and it outputs the actual compound (not its description) the whole process being automatized
  • see Japanese labs on automation
  • ask friends in the pharmaceutic industry
• no mention of Ronald Fisher's The Design of Experiments

Synthesis

So in the end, it was about X and was based on Y.

Critics

Point A, B and C are debatable because of e, f and j.

Vocabulary

(:new_vocabulary_start:) the dew luting sooty pitchblende momentous primeval (:new_vocabulary_end:)

Post-reading model

Draw a schema (using PmGraphViz or another solution) of the situation of the area in the studied domain after having read the book. Link it to the pre-reading model and align the two to help easy comparison.

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